Fade
by DramaLexy
Summary: .'Usually Elizabeth could tell by nine in the morning whether it was going to be a good day...When people started running into her office in a panic before the morning briefing even began, that was a definite sign.'
1. Prologue

TITLE: Fade

AUTHOR: DramaLexy

SUMMARY: "Usually Elizabeth could tell by nine in the morning whether it was going to be a good day...When people started running into her office in a panic before the morning briefing even began, that was a definite sign."

DISCLAIMER: Oh, if only I owned them... grins evilly>> but I don't, so don't sue me.

DISTRIBUTION: Sure, just let me know where so I can come visit

AUTHOR'S NOTE: This is set at some point in the back half of season 2. I'm not sure how specific the spoilers are, but I'll just say that anything before the mid-season finale is fair game.

* * *

Usually Elizabeth could tell by about nine in the morning whether or not it was going to be a good day in Atlantis. Most mornings, any problems that were going to ruin the day would make themselves known in the daily staff meetings that began at that time. When people started running into her office in a panic before that meeting even began, that was a definite sign. 

"What do you mean missing?" she asked Rodney and Zelenka, who were both anxiously standing in her doorway. They exchanged a look.

"There was an experiment I wanted to run before this morning's meeting," Rodney explained.

"WE were going to run," Zelekna interrupted. McKay shot him a Look.

"Harrington and Jennings were supposed to be setting things up in the lab, but no one was there when I arrived. They're not answering calls on headsets, and they're not in their quarters."

Elizabeth frowned. "Weir to Sergeant Bates," she called over her headset. "We've apparently lost contact with a few team members in the city."

"I told Beckett that I would contact you as soon as I had more information," he replied.

"I beg your pardon?"

"He came to me about an hour ago because he couldn't find three of the med-techs." Elizabeth got up.

"Two members of the science staff are missing as well…Get your team on the search and then report to the conference room."

* * *

TBC... 


	2. Chapter 1

It was a small comfort to see that the entire senior staff was present and accounted for. As Elizabeth came into the conference room ten minutes later, everyone was on headsets trying to check in on the status of their team.

"What's the latest?" she asked them.

"Four members of the security team, three med-techs, and two scientists can't be located," Bates told her. Elizabeth could just barely hear John mutter,

"And a partridge in a pear tree," as she sat down.

"Do we know when any of them were seen last?" She asked.

"Yesterday at varying times."

"Well, what has changed in the city between yesterday and today?"

"There was a small energy fluctuation on the south pier yesterday," Bates reported.

"That's where my team was," Rodney replied. He nodded.

"Which is why we didn't think anything of it."

"We need to check out that area," Elizabeth told the security chief. "Did anything unusual happen yesterday?" she asked Rodney. He shook his head.

"We'd found some new labs and were starting to run experiments with the technology. It got late, we all called it a night, and everyone left."

Bates got up. "I'll get a team down there," he said before leaving.

* * *

Six teams of security personnel were quickly organized. Two were going to explore the labs in the south pier, while the other four were going to continue searching the city for their teammates. After getting briefed by Bates, they left for their respective destinations. Walking to the south pier would easily take half an hour at least, so everyone was glad that they had the transporters.

Bates was going with one of the teams to the south pier, so once everyone else was in the transporter, he touched the screen to indicate their destination. The doors closed, then reopened, and they all walked out into the room that they'd arrived in. "McKay said the lab was at the end of the corridor," he told the other men. "We'll start there, and then check out all of the surrounding rooms."

But as they looked around, they realized that they weren't in an area with laboratories. "This looks a lot like the main area on the east pier," one of the officers pointed out as they walked around. Bates looked out the window, up at the city's main spire.

"We are on the east pier," he said as he realized which side of the tower they were looking at. "What the…"

"I'm pretty sure you told the transporter to go to the south pier," one man asserted. Bates shot him a look.

"I know that I hit the main destination on the south pier…There's gotta be a wire crossed or something. Let's try it again."

On the second try, they wound up at the top level of the north pier instead of their desired destination. Bates sighed as he activated his headset. "Sergeant Bates to Dr. McKay: what the hell is going on with the transporters?"

* * *

Elizabeth looked up from her tablet PC at the sound of a knock. John was standing in her open doorway. "We've got a problem," he said.

"We've already got problems," she replied. "What happened now?"

"Bates' teams have gotten lost in the city."

Elizabeth frowned. "They what?"

"There's something wrong with the transporter system; Rodney's working on it. Some were trying to get to the south pier; others were continuing the search for our missing people. The transporters are just arriving at random places, and they've all wound up scattered across the city." Elizabeth sighed.

"Has the whole system been shut off?"

"Yeah. McKay said he'd get you a report within the hour. Bates has one team walking to the south pier, while the others are making their way back to the main spire."

"I want everyone checking in at regular intervals," Elizabeth told him. "We don't need any more people vanishing without a trace."

John nodded. "We're tracking all of them with internal sensors."

"Good."

They both turned as one of the officers that had been out in the control room hurried over to the room. "Excuse me, Dr. Weir? One of the security teams just called in – they're missing people."

John and Elizabeth followed her back out of the room, turning their headsets on. "Where are they?" Elizabeth asked.

The woman pointed on a screen to four blips on the west pier. "That was a six-man team five minutes ago."

"Who's leading the group?" John asked the other officer that was in the room. The younger man was talking with the team on a headset.

"Lieutenant Bell."

"Sheppard to Lieutenant Bell: what's your situation?"

"We were supposed to be searching the low end of the main spire, but got in a transporter and wound up on the west pier. We were walking back, Weston and Carrey were at the back of the group, we turned around and suddenly they were gone."

"You didn't hear or see anything?"

"No, Sir. They just vanished into thin air." Elizabeth and John exchanged a look.

"Get your sixes back here, Lieutenant," he finally said.

"Yes, Sir."

"I want a head count on everyone, now," Elizabeth told John. "Stay in constant contact with all teams that are out in the city," she added for the other officers. They nodded. "And tell Rodney we've got bigger problems at the moment than the fact that the transporters aren't working. I want to know what the hell is happening in this city."

* * *

TBC... 


	3. Chapter 2

**Thanks for the reviews I've gotten so far. I know it's not very shippy yet...I'm working on that. It won't be a straight shipper fic, but there will definitely be something, lol. **

* * *

Everyone was living on pins and needles, not knowing what was going on in Atlantis. By dinnertime, they'd lost nearly twenty team members. Most people stayed in public areas, like the mess hall, so that everyone could keep track of everyone else. People who had to travel between locations went in groups, had to always let someone know where they were going, and then radio in with notification of their successful arrival. 

"I feel like we're back in kindergarten," John said as he, Teyla, and Ronon joined Elizabeth, Rodney, and Beckett in the conference room. Teyla and Ronon shared a look; neither of them had any idea what he was talking about, but decided to let it go.

"We've lost a tenth of our team," Elizabeth told the group. "We have focused sensor data for half of the disappearances and eyewitness reports for almost all of them, so someone please tell me that we're close to finding some answers?"

"There is no logical explanation," Rodney told her. "They simply are spontaneously ceasing to exist."

"What was found in the science labs on the south pier?"

"A few new devices we haven't seen before. I've got people running tests now; I'll let you know what we find once they're done."

"Does anyone have any ideas for a method of protecting ourselves in the meantime?" It was noticeably quiet in the conference room. Everyone looked up as one of the crewmen came running over from the control room.

"There were just some disappearances in the main mess hall," he told Elizabeth. "People...they're getting pretty freaked down down there."

"I'll go check it out," John volunteered. Teyla and Ronon stood as well.

"I want to have another meting in two hours," Elizabeth told them. Everyone nodded before leaving.

* * *

Everybody was edgy as Teyla, Ronon, and John made their way through the city to the mess hall. "Our only option may be leaving the city," Ronon pointed out. 

"We've already tried leaving Atlantis once - things didn't turn out so well," John told him.

"You'd prefer to sit here and wait for the end?"

"I didn't say that," he replied defensively. "It's just that leaving Atlantis may not be as simple of a solution as we'd like to think. And safe worlds may not be as easy to find as you might think."

Ronon shot him a Look. "I know how hard it is." John held the runner's gaze for a moment before nodding.

"You have an opinion, Teyla?" John asked her, turning around. He was surprised to see that she wasn't behind them. "Teyla?" Both men quickly started back down the corridor, but there was no sign of her anywhere. "Sheppard to Weir; Teyla just disappeared."

Elizabeth had been in her office with Beckett and sighed when she heard her 2IC's report. "Understood," she replied. "Continue on to your destination. Let me know when you get there."

"Yes, ma'am."

* * *

Over the next couple of days, their numbers continued to diminish, and no one was any closer to figuring out why. When Elizabeth called a meeting with her senior staff on day four of the crisis, only John, Ronon, and Rodney were still there to attend. And John was finally willing to actually bring up Ronon's suggestion. 

"Leave the city?" Elizabeth asked.

"If something in the city is what's causing us to disappear, then leaving it should stop that," he explained.

"We'd also leave Atlantis unprotected," Elizabeth reminded him, "And that's one experience that I'm not anxious to repeat."

"You'd rather vanish?" Ronon solemnly asked. Elizabeth held his look for a moment.

"That's our last resort," she finally agreed. "Leaving won't solve the problem of what's happened to everyone who has already disappeared. For all we know, they could still be in the city somewhere, and hidden from our sensors."

"Why would the city do that?" John asked.

Elizabeth shrugged, looking to Rodney. The scientist was busily reading over a report and didn't even look up until the city's leader cleared her throat. "Have you found anything new?" she asked him.

"I'm not sure…The last reported disappearance was last night around 7PM," he said, turning around his tablet PC so that everyone could see. "Before that, the longest break was only three hours."

"It's stopped?" John inquired.

"I don't know, but we're now down to about ten percent of the city's original population."

"Let's check in again this afternoon," Elizabeth decided. "Rodney, see what else you can find out, and then we can make a decision as to what to do next."

* * *

Ronon didn't really have a lot of assigned jobs to do in the city; most of his time was spent with whatever John's team was working on, and since SA-1 was most definitely grounded at the moment, he had some free time on his hands. 

He wound up wandering down through the city to the area where the recreational and training rooms were. On most afternoons, if the team wasn't going off-world and there weren't any meetings, he could find Teyla in one of the rooms, having individual or group lessons with her students. Today, however, the training rooms were eerily quiet. Stepping into one of them, Ronon noticed that Teyla had left her gear behind after her last session; he picked up one of her sticks, and started practicing with it. In his mind, he could see the small smile that she'd worn the last time she'd defeated him. They could always go after each other one hundred percent when they trained, putting their almost perfectly-matched skill levels to the test. She'd won their last round, but he would be ready for her next time.

The stick fell from his hand as he realized there might not be a next time. She was gone, and they didn't know…Ronon picked it up again and returned it to it's former location with Teyla's other gear, then turned and left the room without looking back.

* * *

By the time the afternoon meeting was held, there still hadn't been another disappearance since the previous evening. No one knew any better why the vanishings had stopped than they knew why they'd started in the first place. The city was beyond having a skeleton crew; instead of pulling in what was left of her senior staff, Elizabeth got everyone left from the expedition to come to the conference room. There were only nineteen of them. 

"We should start trying to investigate what happened on the south pier again," Rodney argued.

"And what if people start disappearing again?" one of the security personnel inquired.

McKay rolled his eyes. "I don't find the alternative of sitting on our hands and doing nothing to be all that appealing either," he shot back. "This city can't function for any length of time with this few people. There are too many systems, too many things that need monitoring."

"I agree," Elizabeth said. "Organize a team; you can start the search tomorrow. In the meantime – "

A very loud alarm started blaring from the control room, and everyone got to their feet. "What is that?" John asked.

Rodney's eyes were like saucers. "I think it's the self destruct sequence."

* * *

TBC... 

(see the blue button down there? Feedback makes a great holiday gift item!)


	4. Chapter 3

The monitors in the control room displayed the fact that they had a bit less than five minutes before the self destruct went off. John and Elizabeth immediately came forward, putting their codes into the computer to turn it off – and nothing happened. "Try it again," Elizabeth ordered, but the result was the same.

"Do we still have gate control?" John asked one of the crewmen manning the consoles. He hit a chevron, which lit up, and so nodded. "Dial the Alpha Site and everyone get the hell out of here. We'll keep trying to shut it down." Almost everyone ran for the stairs. Rodney was frantically trying to help Elizabeth in shutting down the system. Ronon stayed behind, as did another military officer. "Get out of here, Miller," John told him as he, too, turned back to the computers.

"I may be of help, Sir." No one had time to argue.

"Two minutes," Ronon pointed out as the clock continued to wind down. The Stargate suddenly shut off by itself. After staring down at the gate for a moment, Rodney lunged for the dialing computer. It no longer wanted to respond to anything he did.

"We're stuck here!" he exclaimed. "We're stuck here and about to suffer a fiery death."

"We're not entirely stuck," Sheppard replied. "We've still got jumpers."

"But without the Stargate – " Rodney started to protest.

"We'll still be alive!" John yelled. "Less talking, more running, let's go!"

* * *

No one was looking at watches by the time they got up to the jumper bay – they all knew that time was critically short. John was already halfway into Jumper 2's pilot seat before he realized that Miller, Rodney, and Ronon had gone to Jumper 3. "Miller, what the – " he started to chastise the other pilot over their headsets, then realized it wasn't worth it. "Nevermind. Just get that thing airborne." 

John powered up the Jumper faster than he ever had in his life while Elizabeth sat down beside him. They lifted off of the jumper bay floor and began ascending out of the opening in the ceiling with Jumper 3 right behind them. John could hear the rumble of explosions as the self-destruct initiated. "Come on, come on," he muttered to the Jumper, as though it could hear him, willing it by thought to go faster. Flames shot out of the bay opening below them, desperately trying to lick at the underbelly of the ship. John managed to get enough altitude in time that they avoided them – but Jumper 3 wasn't so lucky. As Atlantis' main spire was engulfed in flames, the second ship disappeared.

"No!" Elizabeth cried, unable to do anything but watch as her dream broke into pieces and slowly began sinking back to the ocean floor. John didn't look down – he didn't think he could handle looking back. He made sure the Jumper continued gaining altitude and flew them away from the remains of the city.

* * *

The ceiling of Atlantis' infirmary wasn't something that most people in the city wanted to see when they woke up. And if Ronon hadn't been so surprised that he was looking at the infirmary ceiling, he probably would have been a little bit more annoyed. 

Looking around, his eyes found Beckett as the doctor made his way through the room, studying some test results. "Doc?"

Beckett looked up, seemingly just as surprised to see his patient conscious as Ronon was to see the doctor alive. "How long have you been awake?" he asked.

"A minute. How are we here? What happened to the self-destruct?"

"There was no self-destruct, lad."

Ronon frowned. "I was looking at the computer – "

"No, you weren't. You were in a type of stasis; everything you've experienced over the past few days – well, past few hours, actually – has been a simulation." The ex-runner understandably looked dubious.

"Simulation?"

"Aye. The first ones to awaken were the ones that figured it out. The device that was found on the south pier managed to knock everyone in the city into a state of suspended animation, while drawing our minds into a shared virtual reality. I believe it must have been similar to the devices on the Aurora, though with a much different purpose."

"What kind of purpose?"

"The simulation would allow the person running it to try out new things within the city without actually having to make the real changes – new power systems or other modifications, simulations of situations like intruders or viruses. It's actually quite ingenious. The problem was: it wasn't activated properly. The system was never designed to be used by so many people at once."

"And that's why people started vanishing from the simulation."

"Aye. As people disappeared from in there, they woke up out here, in the real reality, and put the pieces together. It's been a hell of a morning."

"Morning?" Ronon asked.

"Yes. The simulation doesn't run in real time. What felt like days in there was really only about ten hours."

"How does the simulation get modified? Did you make the city self destruct?" Carson looked down.

"Not intentionally. There were only so many of you left inside, and we were beginning to get concerned. We thought we could remove you all externally from the system by cutting power to the simulation device, but…It was activated improperly."

"You said that already."

"I know…We didn't think it would have such an extreme effect. Colonel Sheppard and Dr. Weir are still inside, and I think we'll be leaving them until we learn more."

Ronon shrugged. "It wasn't all that pleasant, but it was survivable. Why can't you pull them out too?"

"It wasn't survivable for everyone, lad," Carson explained. "You've got a few bumps and bruises and Rodney has a concussion. But Lieutenant Miller…we didn't get him out soon enough. He didn't make it."

* * *

TBC... 


	5. Chapter 4

There was no way, of course, for John and Elizabeth to know what was going on from their spots inside the simulation. All they knew was what they'd seen – they were the two remaining members of the Atlantis expedition.

"We've probably got enough supplies for a week," John told Elizabeth as he took stock of what was packed in the back of the Jumper. The little ship was sitting in high orbit over the planet, with neither of them quite sure what to do next.

"We should have called them over," Elizabeth said.

"What?"

"In the jumper bay. We should have made sure we were all in the same ship."

"If we'd spent another second on the ground, we would all have been dead."

"Right now, Rodney, Ronon, and Miller are dead. And we have no idea what's happened to the people who made it through the Stargate."

"I'm sure they're fine."

"Forgive me if that isn't entirely comforting! Don't you get it, John? With Atlantis gone, everyone who disappeared…"

"Yeah, I get it!" he shot back. "But with just this ship and a handful of MREs, there's really nothing I can do about it at this point. Right now, you and I have to figure out how we're going to stay alive!"

Silence reigned for a long moment. "It'll be another three weeks before the Daedalus returns," Elizabeth finally said. "They're only supposed to be leaving Earth now."

"So we're on our own for a few weeks. We'll ration our supplies."

"Can the jumper last that long?"

"What do you mean?"

"I mean, was it designed to be parked in space for a few weeks and still be able to function? They have to re-power in the jumper bay, don't they?"

"Yeah…we could shut down anything that's non-primary, lower the load for life support…it would be a little chilly in here, and the air would be a bit thin, but nothing worse than Colorado. It might be enough."

"Might?"

"Yeah."

Elizabeth considered that. "Or we could go to the mainland. We wait with the Athosians for the Daedalus."

"It's winter in the Northern Hemisphere," John reminded her.

"I know, and we're not exactly dressed for it, but hopefully they can help with that. They have to be told what's happened anyway." He nodded, moving to sit back down in the pilot's seat.

"Sounds like a plan."

* * *

Back in the real reality, everyone was beginning to recover from their ordeal, even as they worked to figure out what they were going to do with the city's leaders. 

Ronon looked up from the lunch that the med team was forcing him to eat as Teyla came into the infirmary. "I heard that you were awake," she said as she came to his bedside. He sat up a little straighter.

"Yeah, I'm all right…How about you?"

"I am fine; I woke up in my quarters this morning."

"Good. When you disappeared – I mean when everyone was disappearing, we weren't sure if we were going to see them again." Teyla smiled, knowing what he was trying to say.

"We were concerned as well," she told him, "When you – and all the other residents of the city – would not awaken. I am glad you were not seriously injured." Ronon returned her smile. While he was distracted, watching her instead of his plate, she reached to grab a bit of food off of it.

"Hey!" he exclaimed, but Teyla just grinned.

"This, I believe, is called payback," she told him.

"You're stealing food off a sick man's tray?"

Teyla ate the item that she had snatched. "Yes," she replied simply.

* * *

John and Elizabeth's day wasn't getting any better. As they flew over the snow-covered shores of the mainland, they realized that the Athosian settlement wasn't visible. The Athosians had never been part of the simulation in the first place, but they couldn't have known that. The assumption was therefore made that they'd all disappeared already, and the deep snow was masking where their village had been. 

"I think we've got a better chance of keeping life support tolerable if we're down here instead of up there," John said, aiming a finger skyward with the second part of his sentence. "It may be winter, but space is still colder."

Elizabeth nodded, watching as John brought the jumper down. "How many systems can we shut off?"

"Scanners, weapons, engines…I say we exhaust our supply of flashlights and batteries before we use the cabin lights." She nodded.

"We can deal with the dark." John started shutting off everything he'd mentioned.

"There are some extra jackets in the back; I'm going to bring the temperature down to about 5 degrees C." Elizabeth stared.

"Are you serious?"

"We might have to drop it lower later; be glad we've got the extra jackets." She went to look, and returned with the garments a moment later.

"Reminds me of Antarctica," Elizabeth said as she sat back down, looking out the window. John nodded.

"Yeah…I wouldn't mind McMurdo at the moment…"

* * *

They'd each been lying on one of the narrow benches in the back of the jumper when they went to sleep that night, but by morning, they'd both wound up on the floor instead. It was impressively cold, even with their thermal blankets. "What time is it?" Elizabeth asked, noting the fact that she could see her breath when she talked. 

"About nine o'clock," John replied. "I guess this is one morning that you won't be yelling at me for being late to morning briefing." Elizabeth sat up, frowning.

"I don't yell, John."

"Okay, fine. But you have a way of giving people a look that carries volume with it," he replied.

"Comes with the territory. It's useful when trying to get stubborn diplomats to attempt working together…or trying to get inherently late pilots to wake up a few minutes earlier." John rewarded her with his patented flyboy grin.

"Are you hungry?"

"Should we eat now or save it for later?"

"We skipped dinner yesterday, so I think breakfast will be all right."

Elizabeth nodded. "All right, what's on the menu?"

* * *

TBC... 


	6. Chapter 5

For every day that passed in the simulation, only about two hours had gone by in reality. By the time night had fallen in Atlantis, John and Elizabeth had been on the mainland in the simulation for four days.

"I feel like all we do is sleep," Elizabeth commented as she curled up on the floor of the jumper.

"It makes the time pass faster," John pointed out.

"If you say so," she replied, before coughing into her hand.

"You've been doing that all afternoon," he told her. "And you're starting to sound worse."

"I'm fine," Elizabeth tried to tell him. John reached over and felt her forehead.

"You've definitely got a fever."

"It's just a cold. I mean, it's freezing in here." He slid into the pilot's seat and started messing with the controls. "What are you doing?"

"Raising the temperature."

"And then what? When we run out of power, it's going to be even colder than it is now."

John hesitated. "We might not run out."

"No offense, but I don't want to take my chances with 'might'."

"All right…but if you're getting worse tomorrow…"

"Deal." He picked up his blanket and draped it over her on top of the one she already had. "John, what are you doing?" He stopped her from attempting to give the blanket back.

"Trying to make sure you don't freeze. Now go to sleep."

* * *

Beckett looked up from the papers that were spread on his desk when one of the med techs came in the door to his office. "I think we have a problem," the woman said. He followed her back out into the main area of the infirmary. "I went to check on Dr. Weir and Colonel Sheppard – she's got a fever." 

"How high?"

"Almost 102."

Beckett sighed. "All right. Let's run some tests and figure this out."

* * *

It was taking some teamwork to keep things in the city going. Rodney was spending most of his time in the labs working with his team on what to do with the device providing the simulation, but a few threatening looks from Ronon had gotten him to help out with running things in the city. Teyla had picked up a lot of the slack, which didn't sit well with people like Sergeant Bates, but Ronon was always willing to help her out as needed with some good old-fashioned bullying. In all honesty, even Bates could admit that they really didn't have time to argue such things. No one knew when Elizabeth and John would be back to working, and they needed to keep Atlantis running in the meantime. 

The few hours it took for the medical team to run tests were hours that they really couldn't spare. Elizabeth was up to a fever of 104.3 and pneumonia was quickly setting in.

"She was already working herself into the grave before all this started," Beckett told Teyla, Ronon, and Rodney as they had a late-night meeting in the conference room. "What was left of her immune system wasn't able to handle much. To make matters worse, the time difference between the two realities is doubly working against us."

"What do you mean?" Teyla asked.

"Her symptoms are appearing and worsening so quickly that we can barely keep up in this reality."

"But you can treat her for them?" Ronon inquired.

"We tried giving her antibiotics when all she had was bronchitis. In the simulated reality, it takes so long for the medications to work into her system that she already had pneumonia before the antibiotics could do anything. It would seem, at this point, that the only option we have is getting them out of the simulation."

"Preferably without killing them in the process," Rodney pointed out.

"We know now that efforts to cut power to the device affect the scenario that it is creating – we can't try that again unless things get more desperate than they already are."

"What if we don't CUT power," Rodney suggested, "We just REDUCE it?"

"What will that do?" Teyla asked.

"Everyone started disappearing from the simulation in the first place because the device wasn't powerful enough to hold an entire city's worth of people inside."

"Aye," Beckett agreed, "But it can stably hold about twenty or less, and right now it's only got two."

Rodney rolled his eyes. "I'm aware. But what if we get its power levels to the point where it CAN'T even support two?"

"Sheppard and Weir would be forced out of the simulation and wake up," Ronon answered.

Rodney smiled. "Exactly."

* * *

John knew that Elizabeth had gotten much worse in the past three days, but also knew there wasn't much he could do about it without outside help; there wasn't anything in the first aid kits on the Jumper that would do anything for her. He adjusted the temperature inside the jumper when Elizabeth was sleeping, hoping that might help, and made sure she got more of their rations that he did. However, her cough was getting worse, her fever was raging, and he'd never say it out loud, but she looked like hell. 

"Here," John told her, helping her sit up a little from her nest of blankets on the floor and drink the water that he was holding.

"How long was I asleep?" Elizabeth asked.

"A few hours." Her body was wracked with a fit of shivers.

"God, it's so cold," she muttered. He knew it was because of her fever more so than anything else, and while John didn't want to make things worse by totally bundling her up, he wasn't going to just let her freeze. He sat on the floor next to her and pulled away one of the blankets she was tangled up in, then pulled the other one more securely around her and held her close.

"Just think," he said, "When the Daedalus gets here you can go take a hot shower in some quarters for probably an hour or so." Elizabeth smiled.

"That sounds pretty nice right about now. I'm sure this stupid cold will be gone in no time once we get in a…well, a slightly warmer climate." The Daedalus' internal environment was a far cry from summertime in Washington DC, but almost anything was better than what they were currently dealing with.

John tried to smile. "I'm sure," he quietly said.

* * *

TBC... 


	7. Chapter 6

I meant to update a lot sooner, but I was cut off from being able to do so while at home for the holidays. Thanks for being patient with me and for all the reviews I got. Happy New Year!

* * *

Elizabeth fell asleep again soon, and John made his way up to the forward compartment to check on their power supplies. It would be close, but a quick calculation in his head told him that they'd probably be okay until the Daedalus arrived. After eating a very small lunch, he managed to get a short nap of his own, sitting in the pilot's seat. He was awakened, however, by the sound of Elizabeth's voice.

"Why did we stop?" she was asking him. "Have we reached Atlantus?" John got up and headed over to her.

"We're not in Antartica, Elizabeth," he patiently said. "You were just dreaming." She didn't look convinced. Getting up took effort, but she managed to pull herself to her feet, shaking off John's attempts to keep her seated.

"Where are we?" she asked. "Who are you?"

"We're pretty far from home," he admitted. "Remember? Pegasus Galaxy? Atlantis?" Her eyes lost focus.

"John?" she asked in a voice that was so small he could barely hear it.

"Yep. You haven't gotten rid of me yet."

Elizabeth's legs gave out, but he caught her, gently lowering her back down to the floor. "You need to stay put," he told her. "As if you didn't have enough problems already. Wandering around while hallucinating is only wasting energy." He grabbed a container of water and held it up for her.

"The Daedalus isn't going to get here," Elizabeth quietly said after she'd taken a sip. "Not in time."

"Hey. Cut it out. No talking like that in my puddle jumper."

"You can only run from the truth for so long, John."

"I'm serious," he cut her off. "Do I need to annoy you into holding on? Because I can do that, trust me."

Elizabeth smiled slightly. "I don't doubt that."

"We've lost too much already for me to lose you, too. You're not allowed to leave me here by myself…and that's an order, Dr. Weir."

"Are you in charge now?" she asked. John smiled.

"Maybe. Would you follow my orders if I was?"

"Sure…about as well as you follow mine." John pretended to be offended.

"I've gotten a lot better, haven't I?"

"Most days, I'd say yes."

"I see. And is today one of those days?"

Elizabeth smiled. "I'll do everything I can not to leave you here." He returned her grin.

"Good."

* * *

There was a delicate trade-off in the process of removing Elizabeth and John from the simulation. Either they could take time to run analyses and ensure that they wouldn't harm the city's leaders while disconnecting them, gambling with the fact that Elizabeth would live long enough for that, or they could move quickly before she got much worse and gamble with the fact that both of them would survive disconnecting. Carson decided to go with the former idea.

It was almost four AM on a night where most of the science and med team members hadn't slept when they finally decided that they were ready. Rodney's team was down on the south pier with the device, while Beckett's was buzzing around in the infirmary. Ronon and Teyla hovered near the door to the room, waiting for the final outcome of their very long day.

"Dropping power levels," Rodney reported via headset.

"Acknowledged," Carson replied. No one was sure which of them would leave the simulation first, so half the team was around John's bed and the other half surrounded Elizabeth. A monitor beeped as her heart rate began to become unsteady, but a moment later it normalized – and her eyes fluttered open for a moment. Carson began calling orders like a general commanding troops as they rushed to make up for lost time in her treatment.

* * *

John had fallen asleep in the back of the jumper with Elizabeth in his arms, but he woke up to the feeling of a sudden chill. Her overheated body had been helping to keep him warm, but now she was gone.

"Elizabeth?" he said, looking around to see if she'd woken up and, in her delirium, had wandered to the forward compartment, but she wasn't there. She wasn't anywhere in the small ship – she'd vanished into thin air, and John was now alone.

* * *

"We've got Dr. Weir back," Beckett reported to Rodney once she had been stabilized.

"We've got problems," the scientist replied.

"What sort of problems?"

"The device has tapped into a secondary power source – it's running off of completely different systems. We're going to have to figure everything out all over again before we can remove Sheppard."

"How long?"

"Too long," Rodney replied. "Probably a couple days inside the simulation."

"Leaving him alone for two days without any idea of what's happening?"

"We'll work as fast as we can, Carson."

He sighed. "Yes, do that, Rodney."

* * *

It was REALLY quiet in that damn puddle jumper and much colder than it had been before as well. Night had fallen, but John hadn't bothered with a flashlight. He didn't care about sitting in the pitch blackness of the rear compartment.

He wasn't sure exactly when Atlantis had become home. Maybe it had just done so by default due to the fact that for months it had been the only place in the galaxy that they thought safe from the Wraith. He'd almost given his life in order to protect the city – and the planet it was a gateway to – so Atlantis definitely had become home. And the people in it had become family. They were all lost now; he'd believed that he could get Elizabeth to hang on until the Daedalus came, but had never expected her to vanish on him.

"You disobeyed an order, by the way," he said aloud, his voice breaking the heavy silence in the ship. "And yeah, I know, it's not like I never have, but…this was one thing I really needed, Elizabeth."

John suddenly didn't care all that much about saving power in the jumper. He slipped into the pilot's seat and turned everything back on – navigation, scanners, flight controls, and engines. The small ship lifted off of the ground, pulling free of the snow that had fallen on it, and began to climb. Turning back towards the ocean, John flew towards where Atlantis would be floating if the city still existed. He picked a spot where he thought he could still see some debris, then went into a steep climb until he'd reached orbit. He powered the jumper back down again and sat back to wait for the Daedalus.

* * *

The dawn was breaking outside of Atlantis by the time that John was finally pulled from the simulation. Just like the others had, he stared at the infirmary ceiling for a long moment in surprise and disbelief, blinking several times to see if it was still there when his eyes opened.

"Welcome back, Colonel," Beckett told him.

"Yeah, back…where am I?" he asked.

"In Atlantis."

John slowly nodded, not sure whether he could believe that yet, either. "Okay, sure."

"How are you feeling?"

"All right, I think…Am I actually awake? This is real?"

Carson smiled. "Yes, Colonel. You are awake now."

As he turned his head, he caught sight of Elizabeth sleeping in the next bed over. "Is she okay?" he asked. Carson looked over at the expedition's leader as well.

"She will be," he finally answered. John let out a relieved sigh.

"So, Atlantis, huh?" he asked. "I get the feeling I'm about to hear a hell of a story as to what just happened."

* * *

TBC... 


	8. Epilogue

Even after Elizabeth was finally discharged from the infirmary, she was still supposed to be resting for a day or two. It had been almost a week since she'd been up and about in the city, and even longer than that in her mind, so instead of heading for her quarters, she made her way up to the control room and out to her favorite spot on the balcony. She wasn't expecting to see another figure already there.

"When did Carson spring you?" John asked as Elizabeth joined him at the railing.

"Just now. I'm supposed to be 'taking it easy', but…I missed this city." He nodded, watching a smile grace her face as she took in the view.

"Yeah. I know what you mean…At least we have proof that Atlantis won't sink back into the ocean if you aren't working. That means we can force you into taking a break every once in a while now."

"Well, it means you can TRY," she replied with a smile. "And the city managed to function without you as well…although I don't think your team wants to be left in control again any time soon."

"Yeah, probably not."

"I…I wanted to thank you, though."

"For what?"

"Well…for keeping me alive." John shook his head.

"You did that yourself. It's not that easy to get rid of Elizabeth Weir."

"Still…I believed that everything was gone, and I could have given up, if it hadn't been for you."

"Eh, I just couldn't imagine this galaxy without you being here."

Elizabeth smiled. "Likewise. I don't think…that I could run this city without you…and I don't want to have to try."

"Well, I DEFINITELY don't want to have to run this city instead of you, so I think we're even," John replied with a grin.

They were both leaning on the railing, shoulders together, watching the water. John wasn't entirely sure how they wound up with their lips meeting – his brain disengaged almost instantaneously, only to be shifted back out of neutral by the sound of a door opening behind them. Ronon was standing there, a smile that was perhaps a bit too smug on his face.

"We're all here," he told John, who nodded. His team was going off-world to check out possible trading relations with a seemingly friendly planet.

"You want to meet up for dinner tonight?" he quietly asked Elizabeth as they went back inside.

"Does that mean you'll actually be coming back from your mission on time?" she replied with a smile.

"I make no promises."

John joined Ronon, Teyla, and Rodney, who were getting ready to go in the gate room, while Elizabeth made her way up the steps to the control room. Ronon and Teyla were teasing each other over something – John wasn't quite paying attention to them. They had seemed different since he'd woken up, but he hadn't spent a lot of time thinking about it, and right now, there was only one person who he wanted to be contemplating.

Once everyone was finished suiting up, a crewman in the control room started dialing the gate. As the event horizon appeared, John turned back to look for Elizabeth up above them.

"Good luck," she called. John gave her a smile and a wave before following his team out. He would do everything in his power to be back before dinner.

* * *

Fin. 


End file.
